diff limma_voom.xml @ 12:81796eb60bd0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c

--- a/limma_voom.xml	Mon Jun 11 08:18:25 2018 -0400
+++ b/limma_voom.xml	Sun Aug 05 05:13:12 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="limma_voom" name="limma" version="3.34.9.7">
+<tool id="limma_voom" name="limma" version="3.34.9.8">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>
@@ -77,6 +77,10 @@
     -P $out.plots
 #end if
 
+#if $out.filtCounts:
+    -F
+#end if
+
 #if $out.normCounts:
     -x
 #end if
@@ -272,6 +276,10 @@
                 <option value="h">Heatmaps (top DE genes) </option>
                 <option value="s">Stripcharts (top DE genes)</option>
             </param>
+            <param name="filtCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                label="Output Filtered Counts Table?"
+                help="Output a file containing the raw filtered counts if Filter Low Counts is selected. Default: No">
+            </param>
             <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
                 label="Output Normalised Counts Table?"
                 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
@@ -465,9 +473,10 @@
                 </element>
             </output_collection>
         </test>
-        <!-- Ensure normalised counts file output works-->
+        <!-- Ensure filtered and normalised count outputs works-->
         <test>
             <param name="format" value="matrix" />
+            <param name="filtCounts" value="true" />
             <param name="normCounts" value="true" />
             <param name="counts" value="matrix.txt" />
             <repeat name="rep_factor">
@@ -477,19 +486,31 @@
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
+            <param name="filt_select" value="yes" />
+            <param name="format_select" value="counts"/>
+            <param name="cntReq" value="10"/>
+            <param name="count_select" value="sample"/>
+            <param name="cntSampleReq" value="3"/>
             <param name="normalisationOption" value="TMM" />
             <param name="topgenes" value="6" />
-            <output_collection name="outTables" count="2">
+            <output_collection name="outTables" count="3">
                 <element name="limma-voom_Mut-WT" ftype="tabular" >
                     <assert_contents>
                         <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
-                        <has_text_matching expression="11304.*0.4573" />
+                        <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
                     </assert_contents>
                 </element>
                 <element name="limma-voom_normcounts" ftype="tabular" >
                     <assert_contents>
                         <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
-                        <has_text_matching expression="11304.*15.7545" />
+                        <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
+                    </assert_contents>
+                </element>
+                <element name="limma-voom_filtcounts" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
+                        <has_text_matching expression="11304.*361.*397.*346.*356.*312.*337" />
+                        <not_has_text text="11302"/>
                     </assert_contents>
                 </element>
             </output_collection>